I am analysing AS events in Arabidopsis thaliana using SUPPA.
I predicted AS_events using generateEvents option. For calculating PSI (next step), it requires Transcript expression file. But I do not know from where I can get the Transcript expression file for my sample? Can anyone help me in this issue? Thank you in advance

In SUPPA documentation, They have given the following explanation;

The transcript expression file is a tab separated file where each line provides the estimated abundance of each transcript (ideally in TPM units). This file might contain multiple columns with the expression values in different samples. The expression file must have a header with the naming of the different expression fields, i.e., the sample name of each expression value.

Assuming that you either have alignment output (SAM/BAM) or .fastq files, you can generate a count matrix for transcript expression using prepDE.py or featureCounts. You can calculate normalized raw counts or you can calculate TPMs. featureCounts in R will also create a gene length vector which you can use to calculate TPM. Just make sure that you are using transcript as a feature and not gene.